Zo used to be one of my favorite players, while I am mostly indifferent to Howard, but I would say Howard is in the tier just above him.

He's closer to a Pat Ewing than to Alonzo Mourning, and when it's all said and done might be regarded as the Moses of his era (not talking about style of play here, just tiers).
In addition to having led an average team to the NBA Finals at a young age, Dwight is a more dominant presence on the court: not only does he anchor your defense (and it's not just about accumulating blocked shots) but he commands double teams on offense. He's also a better rebounder.

Some will argue that Zo played against better competition (and it's true that so far Dwight has had no one in his conference and only Yao, Gasol and Bynum in the opposing conference), but let's not forget that his career coincided with Shaq who is often criticized for dominating inferior centers.
Even though he played in the same decade, he's not from the same generation as Hakeem, DRob and Ewing - several of his prime years occurred when those were old and washed up.